Chris Gorgolewski
Chris Gorgolewski
As suggested by Trey Smith https://docs.google.com/document/d/1HFUkAEE-pB-angVcYe6pf_-fVf4sCpOHKesUvfb8Grc/edit?disco=AAAABBoxE28 > Here's something that would help JSON novices: for each type of JSON object you describe in your specification, provide a URL to a...
Getting the same thing on WSL (with current master): ``` (base) me@christop:~/workspace/nibabel$ PYTHONPATH=. nosetests -s -v nibabel/tests/test_floating.py nibabel.tests.test_floating.test_type_info ... ok nibabel.tests.test_floating.test_nmant ... ok nibabel.tests.test_floating.test_check_nmant_nexp ... /home/me/workspace/nibabel/nibabel/casting.py:360: RuntimeWarning: overflow encountered in...
on ds000009 R2.0.1 - sub-29 ``` docker run -ti -v D:\:/d bids/broccoli:v1.0.1 /d/data/ds000009_R2.0.1/ /d/scratch/broccoli participant --participant_label 29 Running the BIDS validator for the dataset 1: Not all subjects/sessions/runs have the...
![image](https://user-images.githubusercontent.com/238759/36928618-3ec6aa16-1e3c-11e8-8d9e-9c13adeb0127.png) ds000105/reportlets/fmriprep/sub-5/anat/sub-5_T1w_seg_brainmask.svg This could be solved by applying a denoising algorithm: https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical-imaging/mri-denoising Implemneted as `DenoiseImage` in ANTs
The T1w mask on bbr coregisration plot looks bad ![image](https://user-images.githubusercontent.com/238759/36930951-27169df2-1e61-11e8-8b00-45827dc6349b.png) ds000221/reportlets/fmriprep/sub-010251/ses-01/func/sub-010251_ses-01_task-rest_acq-AP_run-01_bold_bbr.svg Even though it's good on the T1w mask plot ![image](https://user-images.githubusercontent.com/238759/36930956-4b182b94-1e61-11e8-85cc-1f6c2c2c58a3.png) s000221/reportlets/fmriprep/sub-010251/ses-01/anat/sub-010251_ses-01_acq-mp2rage_T1w_seg_brainmask.svg
![image](https://user-images.githubusercontent.com/238759/36172709-8e691dd0-10bb-11e8-8b2e-95274c7d712d.png) https://twitter.com/michaelwaskom/status/963497405726580736
![image](https://user-images.githubusercontent.com/238759/34183046-9d068f7c-e4cd-11e7-8608-5aa1d02a42c9.png) Could be poor data or INU failure. sub-12
Using https://github.com/uw-biomedical-ml/mri2mri
Via link to an external website, top 500 genes passed via URL.